Browse Papers

Search the literature by keyword, topic, or author. Filter to articles with full text available.

3689 results

Full text 2026

Phyling: phylogenetic inference from annotated genomes

Tsai CH, Stajich JE.

Phyling is a fast, scalable, and user-friendly tool supporting phylogenomic reconstruction of species phylogenies directly from protein-encoded genomic data. It identifies orthologous genes by searching protein sequences against a curated set of hidden Markov model …

Read PDF
Bioinformatics
Full text 2025

Complete chloroplast genome analysis of <i>Hypopterygium flavolimbatum</i> Müll. Hal. (Hypopterygiaceae, Bryophyta)

Ye ZK, Yang GY, Tang Y, et al.

To address limited genomic resources hindering <i>Hypopterygium</i> phylogenetics/taxonomy, the chloroplast genome of <i>Hypopterygium flavolimbatum</i> Müll. Hal. (Hypopterygiaceae, Bryophyta) was sequenced. The chloroplast genome is 125,283 bp in length, comprising an 86,845 bp large single-copy region, …

Read PDF
Bioinformatics
Full text 2025

Mitochondrial phylogenomics of pygmy grasshoppers (Orthoptera, Tetrigidae, Metrodorinae): descriptions of a new genus, two new species, and new synonyms from China

Li Y, Leng S, He J, et al.

The Chinese wingless brachypronotal pygmy grasshoppers of the subfamily Metrodorinae have often been classified within the genus <i>Macromotettixoides</i>. In this study, two undescribed species of wingless brachypronotal pygmy grasshoppers belonging to Metrodorinae were collected. To …

Read PDF
Bioinformatics
Full text 2023

A European perspective of phylogenomics, sublineages, geographical distribution, epidemiology, and mutational landscape of mpox virus: Emergence pattern may help to fight the next public health emergency in Europe

Chakraborty C, Bhattacharya M, Saikumar G, et al.

<h4>Background</h4>The 2022 outbreak of the mpox virus (previously monkeypox virus, MPXV) in non-epidemic regions has created a global issue. The emergence of MPXV was first reported in Europe, which was described as the MPXV epicenter, …

Read PDF
Bioinformatics
Full text 2026

Assessment of suitable cultivation area for Paris polyphylla var. chinensis and var. yunnanensis under anthropogenic disturbance based on ensemble modeling and germplasm identification

Wang Y, Liu H, Zhao D, et al.

BACKGROUND: Rhizoma Paridis, a medicinal plant material with significant economic value, is derived from two species: Paris polyphylla var. chinensis (Pc) and var. yunnanensis (Py). However, the challenge in accurately distinguishing these two morphologically similar …

Read PDF
Bioinformatics
Full text 2024

Evolution of plant metabolism: the state-of-the-art

Fernie AR, de Vries S, de Vries J.

Immense chemical diversity is one of the hallmark features of plants. This chemo-diversity is mainly underpinned by a highly complex and biodiverse biochemical machinery. Plant metabolic enzymes originated and were inherited from their eukaryotic and …

Read PDF
Bioinformatics
Full text 2024

Molecular epidemiology of multidrug-resistant &lt;i&gt;Klebsiella pneumoniae, Enterobacter cloacae&lt;/i&gt;, and &lt;i&gt;Escherichia coli&lt;/i&gt; outbreak among neonates in Tembisa hospital, South Africa

Osei Sekyere J, Mmatli M, Bosch A, et al.

<h4>Background</h4>An outbreak of multidrug-resistant <i>Klebsiella pneumoniae, Escherichia coli, and Enterobacter cloacae</i> infections in a neonatal ward within a tertiary hospital in South Africa resulted in the mortality of 10 patients within six months. In this …

Read PDF
Bioinformatics
Full text 2025

A phoenix in the greenhouse: characterization and phylogenomics of complete chloroplast genomes sheds light on the putatively extinct-in-the-wild Solanum ensifolium (Solanaceae)

Graham MR, Kaur N, Jones CS, et al.

<h4>Background</h4>The genus Solanum is a diverse group of flowering plants with significant economic importance. Within this genus, the subgenus Leptostemonum, comprising spiny solanums, is particularly noteworthy due to its high species diversity and endemism. Solanum …

Read PDF
Bioinformatics Structural Variants